[Biopython-dev] Biopython under PyPy

[Eric Talevich]

On Mon, Sep 19, 2011 at 12:33 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Fri, Sep 16, 2011 at 1:07 PM, Peter Cock wrote:
> >>>> What is interesting is running the full test suite reports some
> >>>> false positives (tests which when run on their own, or as part
> >>>> of a smaller group pass), and the test suite itself never finishes:
> >>>> error: Too many open files
> >>>>
> >>>> I'm not sure what this is from... I fixed an obvious handle leak:
> >>>>
> >>>>
> >>>>
> https://github.com/biopython/biopython/commit/f7ce81b3751745970c32cc813836507e93da3c30
> >>>>
> >>>> I suspect the problem is some of the individual tests are
> >>>> leaking handles - which we know already from warnings
> >>>> under Python 3 etc.
>
> Adding a gc.collect() call after each test_XXX.py is run
> seems to solve that in as much as run_tests.py finishes.
>
> We're down to these failures,
>
> test_CAPS.py
> test_Pathway.py
> test_Restriction.py
> test_SeqIO_index.py - leaking handles
>
> I'll look at test_SeqIO_index.py a bit more, but the others
> are more curious. They could indicate some fragile code
> in Biopython which is implementation specific, or perhaps
> they hit a bug in PyPy. Is anyone interested in finding out?
>
> Otherwise we can skip them for now, so that the whole
> test suite passes, and get PyPy added to the BuildBot
> for nightly regression testing.
>

I could take a look at test_Restriction.py this weekend, I think.

-Eric